BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy1016
(718 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3FQD|A Chain A, Crystal Structure Of The S. Pombe Rat1-Rai1 Complex
Length = 899
Score = 384 bits (986), Expect = e-106, Method: Compositional matrix adjust.
Identities = 199/371 (53%), Positives = 258/371 (69%), Gaps = 14/371 (3%)
Query: 2 GVPAFFRWLSRKYPSVIVHCVEDKPQEV-NGQKIPFDSSKPNPNGMEFDNLYLDMNGIIH 60
GVPA FR LSRK+ VI +E +++ +G +I D S PNPNG+E DNLYLD NGI+H
Sbjct: 5 GVPALFRLLSRKFAKVITPVIEAPTEKLPDGTEIEPDLSLPNPNGVECDNLYLDXNGIVH 64
Query: 61 PCTHPEDKPAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQQRSRRFR 120
PC+HPED+PAP+ EDE VA+FE DR+ VRPR+LL++AIDGVAPRAK NQQRSRRFR
Sbjct: 65 PCSHPEDRPAPETEDEXXVAVFEYTDRILAXVRPRQLLFIAIDGVAPRAKXNQQRSRRFR 124
Query: 121 ASKETAEKIAEVARIREKLLADGCILPPEKEKGSHFDSNCITPGTPFMARLSACLHYYIH 180
+S+E A K E+ E+ G + K +DSNCITPGTPF L+ L YYI
Sbjct: 125 SSREAALKEEELQAFIEEAKQQGIPIDENATKKKSWDSNCITPGTPFXDTLAKSLRYYII 184
Query: 181 DRLNNDPGWKGIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADADLIML 240
++LN+DP W+ ++ ILSDA+VPGEGEHKI ++IR QR +P++DPNT H + G DADLI L
Sbjct: 185 NKLNSDPCWRNVRFILSDASVPGEGEHKIXEFIRSQRVKPEYDPNTHHVVYGLDADLIXL 244
Query: 241 GLATHEPNFTIIREEFKPNQARPCDVCGQMGHEMK---ECVGLDAEPNPESVITFGSEVE 297
GLATHEP+F ++RE DV Q G K E +G+ + +
Sbjct: 245 GLATHEPHFRVLRE----------DVFFQQGSTKKTKEERLGIKRLDDVSETNKVPVKKP 294
Query: 298 FIFVRLSVLREYLEKELAMPNLPFPYSFERALDDWVFMCFFVGNDFLPHLPSLEIREGAV 357
FI++ +S+LREYLE EL +PNLPFP+ ERA+DDWVF FFVGNDFLPHLPSL+IR+GAV
Sbjct: 295 FIWLNVSILREYLEVELYVPNLPFPFDLERAIDDWVFFIFFVGNDFLPHLPSLDIRDGAV 354
Query: 358 DRLVNLYKKTV 368
+RL +++ ++
Sbjct: 355 ERLTEIWRASL 365
Score = 106 bits (265), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 46/79 (58%), Positives = 58/79 (73%), Gaps = 2/79 (2%)
Query: 408 VRLWEDGFKDRYYESKFDV-PKDDIAFRLMVGHEYVLGLCWVLKYYYQGCRSWKWYFPFH 466
VRL+E G+++RYYE KF + P + R V H YV GLCWVL YYYQGC SW WY+P+H
Sbjct: 587 VRLYEPGYRERYYEQKFHISPDEPEKIREAVKH-YVHGLCWVLLYYYQGCPSWTWYYPYH 645
Query: 467 YAPFASDFINIAEVDTNFE 485
YAPFA+DF ++A +D FE
Sbjct: 646 YAPFAADFKDLASIDVKFE 664
Score = 79.0 bits (193), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 36/55 (65%), Positives = 45/55 (81%)
Query: 664 QDSPIIDFYPEDFKIDLNGKKFAWQGVALLPFVDEERLHKALAPYYEKLSVEESE 718
++S IIDFYPE+F IDLNGKKF WQGVALLPF+DE RL A++ Y +L+ EES+
Sbjct: 698 ENSEIIDFYPENFTIDLNGKKFEWQGVALLPFIDENRLLNAVSKIYPQLTEEESK 752
Score = 37.4 bits (85), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 24/36 (66%)
Query: 591 GFLTDSGDVKLERVQLIMQDLGMMEDEIFKKRQQTE 626
G+LT G V L R ++I+ +G ED+IFK+ +Q E
Sbjct: 370 GYLTLDGSVNLARAEVILSAVGNQEDDIFKRLKQQE 405
>pdb|3PIE|A Chain A, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIE|B Chain B, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIE|C Chain C, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIE|D Chain D, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIF|A Chain A, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
pdb|3PIF|B Chain B, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
pdb|3PIF|C Chain C, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
pdb|3PIF|D Chain D, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
Length = 1155
Score = 299 bits (766), Expect = 3e-81, Method: Compositional matrix adjust.
Identities = 159/372 (42%), Positives = 220/372 (59%), Gaps = 59/372 (15%)
Query: 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIH 60
MG+P FF ++S ++P + Q ++G +IP EFDNLYLDMN I+H
Sbjct: 1 MGIPKFFHFISERWPQI--------SQLIDGSQIP-----------EFDNLYLDMNSILH 41
Query: 61 PCTHPEDKPAPK--DEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQQRSRR 118
CTH + E+E+ IF ID LF ++P++ YMAIDGVAPRAKMNQQR+RR
Sbjct: 42 NCTHGDGSEVNSRLSEEEVYSKIFSYIDHLFHTIKPKQTFYMAIDGVAPRAKMNQQRARR 101
Query: 119 FRASKETAEKIAEVARIREKLLADGCILPPEKEKGSHFDSNCITPGTPFMARLSACLHYY 178
FR + + + + +K + +G LP KG FDSN ITPGT FMA+L+ L Y+
Sbjct: 102 FRTAMDAEKAL-------QKAIENGDELP----KGEPFDSNAITPGTEFMAKLTENLKYF 150
Query: 179 IHDRLNNDPGWKGIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADADLI 238
IHD++ ND W+ +KVI S VPGEG+HKIMDYIR RAQ D++PNT+HC+ G DADLI
Sbjct: 151 IHDKITNDTRWQNVKVIFSGHEVPGEGQHKIMDYIRAIRAQEDYNPNTRHCIYGLDADLI 210
Query: 239 MLGLATHEPNFTIIREEFKPNQARPCDVCGQMGHEMKECVGLDAEPNPESVITFGSEVEF 298
+LGL+TH+ +F ++REE G L+ + F
Sbjct: 211 ILGLSTHDHHFCLLREEV------------TFGKRSSSVKTLETQ-------------NF 245
Query: 299 IFVRLSVLREY--LEKELAMPNLPFPYSFERALDDWVFMCFFVGNDFLPHLPSLEIREGA 356
+ LS+LREY LE E ++ F Y FER LDD++F+ F +GNDFLP+LP L +++GA
Sbjct: 246 FLLHLSILREYLALEFEEITDSVQFEYDFERVLDDFIFVLFTIGNDFLPNLPDLHLKKGA 305
Query: 357 VDRLVNLYKKTV 368
L+ +K+ +
Sbjct: 306 FPVLLQTFKEAL 317
Score = 71.2 bits (173), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 34/76 (44%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 415 FKDRYYESKFDVPKDDIAFRLMVGHEYVLGLCWVLKYYYQGCRSWKWYFPFHYAPFASDF 474
+KD+YY+ K D +D + YV GL WVL YYY+GC SW WY+ +HYAP SD
Sbjct: 491 WKDQYYKDKLDFSINDTDSLKEMTENYVGGLQWVLYYYYRGCPSWSWYYRYHYAPRISDV 550
Query: 475 INIAEVDTNFETGTQP 490
I + + F G QP
Sbjct: 551 IKGIDQNIEFHKG-QP 565
Score = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 27/55 (49%), Positives = 40/55 (72%)
Query: 664 QDSPIIDFYPEDFKIDLNGKKFAWQGVALLPFVDEERLHKALAPYYEKLSVEESE 718
+ SPI+DFYP + ++DLNGK W+ V + FVD++RL +A+APY KLS +E +
Sbjct: 595 EHSPILDFYPNEVELDLNGKTADWEAVVKISFVDQKRLVEAMAPYDAKLSPDEKK 649
>pdb|2Y35|A Chain A, Crystal Structure Of Xrn1-Substrate Complex
Length = 1140
Score = 281 bits (720), Expect = 6e-76, Method: Compositional matrix adjust.
Identities = 156/367 (42%), Positives = 208/367 (56%), Gaps = 60/367 (16%)
Query: 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIH 60
MGVP FFR++S +YP C+ + +E IP EFDNLYLDMNGI+H
Sbjct: 1 MGVPKFFRYISERYP-----CLSELARE---HCIP-----------EFDNLYLDMNGIVH 41
Query: 61 PCTHPEDKPAP--KDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQQRSRR 118
C+HP+D +E+++ IF +D+LF +++P++L ++++DGVAPRAKMNQQRSRR
Sbjct: 42 NCSHPDDNNIHFHLEEEQIFQEIFNYVDKLFYLIKPQRLFFLSVDGVAPRAKMNQQRSRR 101
Query: 119 FRASKETAEKIAEVARIREKLLADGCILPPEKEKGSHFDSNCITPGTPFMARLSACLHYY 178
FR ++E ++ A+ A+ E + FDSNCITPGT FM RL L +
Sbjct: 102 FRTAREAEQQEAKAAQ------------RGELREHERFDSNCITPGTEFMVRLQEGLRAF 149
Query: 179 IHDRLNNDPGWKGIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADADLI 238
+ +++ DP W+ VILS PGEGEHKIMDYIR + QPD+DPNT+HCL G DA LI
Sbjct: 150 LKTKISTDPLWQRCTVILSGQEAPGEGEHKIMDYIRYMKTQPDYDPNTRHCLYGLDAALI 209
Query: 239 MLGLATHEPNFTIIREEFKPNQARPCDVCGQMGHEMKECVGLDAEPNPESVITFGSEVEF 298
+LGL THE +F ++REE K G +K T E F
Sbjct: 210 ILGLCTHELHFVVLREEVK------------FGRNVKR--------------TSVEETRF 243
Query: 299 IFVRLSVLREYLEKEL-AMPNLPFPYSFERALDDWVFMCFFVGNDFLPHLPSLEIREGAV 357
+ L +LREYLE E A+ + +DDWV M F VGNDF+PHLP L I A+
Sbjct: 244 FLLHLGLLREYLELEFDALRTDEHKLDIAQLIDDWVLMGFLVGNDFIPHLPCLHISSNAL 303
Query: 358 DRLVNLY 364
L Y
Sbjct: 304 PLLYRTY 310
Score = 77.4 bits (189), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 36/76 (47%), Positives = 46/76 (60%), Gaps = 3/76 (3%)
Query: 414 GFKDRYYESKFDV-PKDDIAFRLMVGHEYVLGLCWVLKYYYQGCRSWKWYFPFHYAPFAS 472
+K +Y +KF P D++ L H YV L WVL YYY+G +SW WY+PFHY PF S
Sbjct: 413 NYKRNFYRNKFKRDPNDELIEELC--HHYVNALQWVLDYYYRGVQSWDWYYPFHYTPFIS 470
Query: 473 DFINIAEVDTNFETGT 488
D NI +V+ F GT
Sbjct: 471 DLKNIEQVEIAFHMGT 486
Score = 62.4 bits (150), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 28/53 (52%), Positives = 38/53 (71%)
Query: 666 SPIIDFYPEDFKIDLNGKKFAWQGVALLPFVDEERLHKALAPYYEKLSVEESE 718
SP+ +FYP +F+ DLNGKK W+ V L+PF+DE RL A+ P +LS+EE E
Sbjct: 519 SPLAEFYPLEFESDLNGKKHDWEAVVLIPFIDEGRLLAAMLPCEAQLSLEERE 571
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.322 0.139 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,026,121
Number of Sequences: 62578
Number of extensions: 877104
Number of successful extensions: 1509
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1485
Number of HSP's gapped (non-prelim): 12
length of query: 718
length of database: 14,973,337
effective HSP length: 106
effective length of query: 612
effective length of database: 8,340,069
effective search space: 5104122228
effective search space used: 5104122228
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)